Journal: Journal of Korean Medical Science

Article Title: Immune Responses After Vaccination With Primary 2-Dose ChAdOx1 Plus a Booster of BNT162b2 or Vaccination With Primary 2-Dose BNT162b2 Plus a Booster of BNT162b2 and the Occurrence of Omicron Breakthrough Infection

doi: 10.3346/jkms.2023.38.e155

Figure Lengend Snippet: WT = wild type, SVNT = surrogate virus neutralization test, IGRA = interferon-γ release assay.

Article Snippet: Neutralizing antibody responses against wild type SARS-CoV-2 were detected using the GenScript SARS-CoV-2 cPass surrogate virus neutralization test (SVNT-WT) kit (GenScript Biotech Corporation, Piscataway, NJ, USA).

Techniques: Virus, Neutralization, Release Assay

Journal: Journal of Korean Medical Science

Article Title: Immune Responses After Vaccination With Primary 2-Dose ChAdOx1 Plus a Booster of BNT162b2 or Vaccination With Primary 2-Dose BNT162b2 Plus a Booster of BNT162b2 and the Occurrence of Omicron Breakthrough Infection

doi: 10.3346/jkms.2023.38.e155

Figure Lengend Snippet: SVNT = surrogate virus neutralization test, BNT = BNT162b2, ChAdOx = ChAdOx1 nCoV-19. To adjust the effect of the time-difference in comparing the serologic test results between the two groups, the comparison in ( A ) was not different ( P = 0.704), but that in ( B ) was different ( P = 0.001) in multiple regression models * .

Article Snippet: Neutralizing antibody responses against wild type SARS-CoV-2 were detected using the GenScript SARS-CoV-2 cPass surrogate virus neutralization test (SVNT-WT) kit (GenScript Biotech Corporation, Piscataway, NJ, USA).

Techniques: Virus, Neutralization, Comparison

Journal: Journal of Korean Medical Science

Article Title: Immune Responses After Vaccination With Primary 2-Dose ChAdOx1 Plus a Booster of BNT162b2 or Vaccination With Primary 2-Dose BNT162b2 Plus a Booster of BNT162b2 and the Occurrence of Omicron Breakthrough Infection

doi: 10.3346/jkms.2023.38.e155

Figure Lengend Snippet: SVNT = surrogate virus neutralization test, IGRA = interferon-γ release assay, BI = breakthrough infection.

Article Snippet: Neutralizing antibody responses against wild type SARS-CoV-2 were detected using the GenScript SARS-CoV-2 cPass surrogate virus neutralization test (SVNT-WT) kit (GenScript Biotech Corporation, Piscataway, NJ, USA).

Techniques: Virus, Neutralization, Release Assay, Infection

Journal: The Journal of Cell Biology

Article Title: Structural, super-resolution microscopy analysis of paraspeckle nuclear body organization

doi: 10.1083/jcb.201601071

Figure Lengend Snippet: Core-shell arrangement of protein components in paraspeckle spheres I. (A) Simultaneous detection of Neat1 and seven of the protein components of paraspeckles, including Sfpq, Nono, Pspc1, Fus, Rbm14, Brg1, and Tardbp in corpus luteal cells. Note that the paraspeckle proteins are grouped into the core, patch, and shell components depending on their distribution in the paraspeckles. (B) Dendrogram based on pairwise class-distance matrix generated using the machine-learning pattern-recognition tool wndchrm. The shell, core, and patch components are grouped into three distinct branches. (C) A model for the structure of paraspeckles. Neat1 folds in half with the 5′ and the 3′ regions bundled independently and radially arranged to construct scaffolds of paraspeckles. Bar, 500 nm.

Article Snippet: For the simultaneous detection of paraspeckle proteins, the following antibodies were used: mouse mAb against Sfpq (clone B92; Abcam), mouse mAb against Nono , mouse mAb against Pspc1 (clone 1L4; Sigma-Aldrich), mouse mAb against Fus (clone 4H11; Santa Cruz Biotechnology, Inc.), rabbit polyclonal antibody against Fus (ab84078; Abcam), rabbit polyclonal antibody against Brg1 (A300-813A; Bethyl Laboratories, Inc.), rabbit polyclonal antibody against Tardbp (10782-2-AP; Proteintech), and rabbit polyclonal antibody against Rbm14 (A300-311A; Bethyl Laboratories, Inc.).

Techniques: Generated, Construct

Journal: The Journal of Cell Biology

Article Title: Structural, super-resolution microscopy analysis of paraspeckle nuclear body organization

doi: 10.1083/jcb.201601071

Figure Lengend Snippet: Core-shell arrangement of protein components in paraspeckle spheres II. Higher magnification SIM images of two of the representative single paraspeckles stained with the Neat1 5′+3 ′ probe and Sfpq (A), Nono (B), Pspc1 (C), Fus (D), Rbm14 (E), Brg1 (F), and Tardbp (G). Intensity profiles along the dashed lines (a and b) are shown in the graphs next to the images. Bar, 100 nm.

Article Snippet: For the simultaneous detection of paraspeckle proteins, the following antibodies were used: mouse mAb against Sfpq (clone B92; Abcam), mouse mAb against Nono , mouse mAb against Pspc1 (clone 1L4; Sigma-Aldrich), mouse mAb against Fus (clone 4H11; Santa Cruz Biotechnology, Inc.), rabbit polyclonal antibody against Fus (ab84078; Abcam), rabbit polyclonal antibody against Brg1 (A300-813A; Bethyl Laboratories, Inc.), rabbit polyclonal antibody against Tardbp (10782-2-AP; Proteintech), and rabbit polyclonal antibody against Rbm14 (A300-311A; Bethyl Laboratories, Inc.).

Techniques: Staining

Journal: The Journal of Cell Biology

Article Title: Structural, super-resolution microscopy analysis of paraspeckle nuclear body organization

doi: 10.1083/jcb.201601071

Figure Lengend Snippet: Fus-independent and dependent recruitment of paraspeckle proteins. (A) Simultaneous detection of Neat1 and seven of the protein components of paraspeckles, including Sfpq, Nono, Pspc1, Fus, Rbm14, Brg1, and Tardbp, in MEFs derived from WT and Fus KO mice. Note that DBHS family proteins (Sfpq, Nono, and Pspc1) and Tardbp, but not Rbm14 and Brg1, are recruited to the putative transcription site in the absence of Fus. Arrowheads indicate paraspeckle-like nuclear bodies formed at the putative Neat1 transcription site in Fus KO MEFs. (B) Simultaneous detection of various forms of NEAT1 and NONO in HAP1 cells and FUS-deleted HAP1 cells (ΔFUS HAP1). Probes used to detect NEAT1 are shown in the top boxes. (C) Schematic drawing of full-length and mutant FUS protein exogenously expressed by lentiviruses. ΔN FUS lack the PrLD and ΔC FUS lack the RNA binding domains including RNA recognition motifs (RRM) and arginine (R)-glycine-glycine domain (RGG) as well as zinc finger domain (ZF). (D) Western blot analyses of lysate from the cells infected with control EGFP (C), full-length FUS (FL), ΔN FUS (ΔN), and ΔC FUS (ΔC). Note that migration of FL and ΔN are much slower than predicted molecular mass (57 and 35 kD, respectively), probably because of the presence of PrLD in these molecules. (E) Simultaneous detection of Neat1 5′+3′ and Nono in Fus KO MEFs expressing various forms of FUS protein. Note that the core-shell structure of paraspeckles was rescued with FL FUS, but not with mutant molecules that lack either PrLD or RNA binding domains. (F) Confirmation of the specificity of polyclonal [Fus (poly)] and monoclonal (Fus) antibodies against Fus. Mixtures of MEFs derived from WT and KO mice of Fus were stained with each antibody. Note the complete absence of signals in the Fus KO MEFs (arrowheads). The positions of the epitope of these antibodies are shown in the schematic drawing of the domain structure of Fus. (G) Simultaneous detection of Fus using polyclonal antibodies and mAbs that recognize the N- and C-terminal region of the protein, respectively. Bars: (A, B, E, and G) 500 nm; (F) 200 µm.

Article Snippet: For the simultaneous detection of paraspeckle proteins, the following antibodies were used: mouse mAb against Sfpq (clone B92; Abcam), mouse mAb against Nono , mouse mAb against Pspc1 (clone 1L4; Sigma-Aldrich), mouse mAb against Fus (clone 4H11; Santa Cruz Biotechnology, Inc.), rabbit polyclonal antibody against Fus (ab84078; Abcam), rabbit polyclonal antibody against Brg1 (A300-813A; Bethyl Laboratories, Inc.), rabbit polyclonal antibody against Tardbp (10782-2-AP; Proteintech), and rabbit polyclonal antibody against Rbm14 (A300-311A; Bethyl Laboratories, Inc.).

Techniques: Derivative Assay, Mutagenesis, RNA Binding Assay, Western Blot, Infection, Control, Migration, Expressing, Staining

Journal: Cell Death & Disease

Article Title: The novel c-Met inhibitor cabozantinib overcomes gemcitabine resistance and stem cell signaling in pancreatic cancer

doi: 10.1038/cddis.2013.158

Figure Lengend Snippet: Long-term treatment with cabozantinib changes the level of anti- and pro-apoptotic proteins. ( a ) Proteins were isolated from parental BxPc-3 cells and the derived subclone XL-7. Binding of proteins to antibodies spotted in duplicate to the membrane of a Human Apoptosis Array was detected using biotinylated secondary antibodies, streptavidin-HRP and chemiluminescence. The pixel density was quantified using ImageJ software and normalized to the mean pixel intensity of the reference spots A1, A12 and E1 on the membrane. Spot D12 is the PBS-negative control. ( b ) mRNA from parental BxPc-3 cells and derived subclones XL-1 to XL-7 was harvested and expression of Bcl-2 and Survivin were examined by qRT-PCR. ( c ) Likewise, expression of anti-apoptotic (Bcl-2, Survivin, XIAP, cIAP2) and pro-apoptotic (p53, Bim) proteins were examined by western blot analysis

Article Snippet: The following antibodies were used: Mouse mAb against human XIAP (BD Biosciences, San Jose, CA, USA), rabbit mAb against human c-Met, SOX2, p53 (Cell Signaling, Danvers, MA, USA), Ki67 (Epitomics, Burlingame, CA, USA), rabbit pAb against human Bcl-2 (Cell Signaling), Bim (Abcam, Cambridge, UK), cIAP2 (Epitomics), survivin and p-Met (R&D Systems, Minneapolis, MN, USA).

Techniques: Isolation, Derivative Assay, Binding Assay, Software, Negative Control, Expressing, Quantitative RT-PCR, Western Blot

Journal: PLoS Pathogens

Article Title: Synergistic Induction of Interferon α through TLR-3 and TLR-9 Agonists Identifies CD21 as Interferon α Receptor for the B Cell Response

doi: 10.1371/journal.ppat.1003233

Figure Lengend Snippet: (A) Spleen cells from cotton rats were stimulated with Concanavalin A for 72 hours and lymphoblasts purified by centrifugation on a ficoll-gradient. Subsequently, cells were stained with antisera specific for the human interferon receptor to test for crossreactive binding to cotton rat cells and analyzed by flow cytometry. Antibody specific for human interferon alpha receptor-1 (IFNAR-1) did not react with cotton rat cells (left) whereas antibody specific for human interferon alpha receptor-2 (IFNAR-2) did (right). IFNR specific antibody is shown as black line, controls as gray areas. B. IFNAR-2 antibody was added to cotton rat spleen cells. One hour later different concentrations of a combination of ODN2216 and poly I:C was added. 24 hours later supernatant was harvested and tested for the presence of type I interferon. The data is combined from two independent experiments. Significant differences were seen between cells treated with the combination of ODN2216 and poly I:C alone, or the combination of ODN2216 and poly I:C with antibody. IFNAR-1 antibody (not reactive with cotton rat cells) had no effect. C. Cotton rat spleen cells were stimulated with ODN 2216 or poly I:C, with or without the addition of recombinant cotton rat interferon alpha. (One unit equals one picogram of type I interferon.) 24 hours later supernatant was harvested and tested for the presence of type I interferon. The data is combined from two independent experiments, and significance was compared to cells without type I interferon treatment. Statistical analysis was done by ANOVA (* p<0.05, ** p<0.01, *** p<0.001).

Article Snippet: Neutralizing goat antibodies against cotton rat interferon alpha and IL-6 were purchased from R&D systems.

Techniques: Purification, Centrifugation, Staining, Binding Assay, Flow Cytometry, Recombinant

Journal: PLoS Pathogens

Article Title: Synergistic Induction of Interferon α through TLR-3 and TLR-9 Agonists Identifies CD21 as Interferon α Receptor for the B Cell Response

doi: 10.1371/journal.ppat.1003233

Figure Lengend Snippet: A) The number of MeV-specific B cells was measured from bone marrow cells of MeV-immune cotton rats. The addition of ODN 2216 and poly I:C individually and in combination increased B cell numbers whereas the addition of sera neutralizing cotton rat interferon alpha and IL-6 reduced this stimulation. Each bar graph represents the mean ± SD of triplicate wells. B) Cotton rats were immunized intranasally (upper panel) or subcutaneously (lower panel) with MeV, or MeV with ODN 2216 and/or pI:C in the presence or absence of human MeV-specific IgG (neutralization titer of 100) which had been injected intraperitoneally one day before immunization. Sera were collected at seven weeks post vaccination and the titer of neutralizing antibody was determined by neutralization assay. Each bar graph represents the average titer of four animals ± SD. The experiment is representative of three experiments. Statistical analysis was done by ANOVA (* p<0.05, ** p<0.01, *** p<0.001).

Article Snippet: Neutralizing goat antibodies against cotton rat interferon alpha and IL-6 were purchased from R&D systems.

Techniques: Neutralization, Injection